GapMind for catabolism of small carbon sources

 

Protein 3607686 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_1095 aldehyde dehydrogenase (RefSeq)

Length: 506 amino acids

Source: Dino in FitnessBrowser

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 77% 97% 791.6 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 716.5
2'-deoxyinosine catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 77% 97% 791.6 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 716.5
2-deoxy-D-ribose catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 77% 97% 791.6 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 716.5
ethanol catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 77% 97% 791.6 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 716.5
L-threonine catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 77% 97% 791.6 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 716.5
thymidine catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 77% 97% 791.6 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 716.5
L-tryptophan catabolism adh hi Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized) 77% 97% 791.6 NAD+-dependent secondary alcohol dehydrogenase III monomer 69% 716.5
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 372.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 372.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 92% 365.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 349.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 349.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 95% 349.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 336.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 336.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 97% 336.7 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-tryptophan catabolism nbaE lo 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 40% 98% 349.4 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-arginine catabolism kauB lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 99% 340.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-arginine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 99% 340.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-citrulline catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 99% 340.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
putrescine catabolism puuC lo 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 39% 99% 340.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 37% 99% 300.1 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 99% 283.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 99% 283.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 99% 283.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 36% 99% 283.9 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 98% 221.5 Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 77% 791.6

Sequence Analysis Tools

View 3607686 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNEMTQVDDTLVSPFKDRYDNFIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVEL
ALDAAHAAKDAWGKTSVTERANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPL
AVDHFRYFAGVLRGQEGSMSEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIA
AGNCIVLKPAEQTPAAIMVLVELISDLLPAGVLNIVNGYGGEVGAALATSDRIAKIAFTG
STATGRKIMEAATVNLIPVTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAFNQGEV
CTCPSRALIHEDIYEEFIARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGV
EEGAEVLTGGKVADVSDDLKDGFYIEPTILKGHNKMRVFQEEIFGPVVSVTTFKTEEEAL
ELANDTMYGLGAGVWSRDQNTCYRFGRGVQAGRVWVNNYHAYPAHAAFGGYKQSGIGREN
HKMMLDHYQQTKNMLVSYNPNKLGFF

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory